The control of mRNA translation into proteins is critical for the adaptation of eukaryotic cells to environmental changes and stress conditions.Glucose starvation in yeast is one of the prototypical eukaryotic stresses. Early translation-mediated gene expression changes in glucose starvation are critically important to trigger the subsequent events leading to transcriptional reprogramming, but the mRNAs involved and the mechanisms of their selective regulation remain obscure.
We analysed glucose-specific translational control by Translation Complex Profile sequencing (TCP-seq). TCP-seq measures the footprints of ribosomal complexes along mRNA using a combination of in vivo fixation, complex purification and high-throughput sequencing. Here, to dissect different aspects of translation regulation, we separately recorded footprints of single ribosomes and disomes. We furthermore sequenced footprints of three distinct complexes involving small ribosomal subunits (SSU), those derived from polysomes,polysome-freeSSUs,and SSUs that selectively contained the scanning translation initiation factor eIF4A.
Upon extended starvation, we observe a shift to the alcohol as a source of nutrition. Promoter analysis of the regulated transcripts clusters revealed presence of motifs indicative of modulating expression of ribosomal protein and biogenesis (RiBi) genes. RiBi expression adjustment is consistent with cell growth, stress and nutrient starvation response.The results suggest that already early in the response several major pathways are involved in the translational control simultaneously, as mRNAs are specifically degraded or preserved and their translation is selectively shut down, unperturbed or upregulated. In the extremely rapid response and using innovative, accurate translation rate measurements, we observe an increased level of translation of many glucosynthetic mRNAs, such as encoding glucokinase, hexokinase, 3-phosphoglycerate kinase and mRNAs encoding heat shock proteins.
Overall, our data uncovers a complex picture of rapid translational changes and present a collection of transcripts involved in the acute response.